Single-cell transcriptome and metagenome profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants

Abstract

The rumen undergoes developmental changes during maturation. To characterize this understudied dynamic process, we profiled single-cell transcriptomes of about 308,000 cells from the rumen tissues of sheep and goats at 17 time points. We built comprehensive transcriptome and metagenome atlases from early embryonic to rumination stages, and recapitulated histomorphometric and transcriptional features of the rumen, revealing key transitional signatures associated with the development of ruminal cells, microbiota, and core transcriptional regulatory networks. In addition, we identified and validated potential cross-talk between host cells and microbiomes and revealed their roles in modulating the spatiotemporal expression of key genes in ruminal cells. Cross-species analyses revealed convergent developmental patterns of cellular heterogeneity, gene expression, and cell–cell and microbiome–cell interactions. Finally, we uncovered how the interactions can act upon the symbiotic rumen system to modify the processes of fermentation, fiber digestion, and immune defense. These results significantly enhance understanding of the genetic basis of the unique roles of rumen.

Single-Cell Sequencing Technology in Ruminant Livestock: Challenges and Opportunities

“…Single-cell sequencing, including sc/snRNA-seq and sc/snATAC-seq, is a powerful tool that provides insights into cellular heterogeneity, gene expression profiles across cell types, and regulatory networks. The most commonly used platform for single-cell sequencing in ruminant livestock is currently 10× Genomics Chromium [ 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 ]. The 10× Genomics Chromium workflow for sc/snRNA-seq broadly entails cell or nuclei isolation, encapsulation of cells or nuclei in oil droplets with barcoded beads using microfluidics, cell and/or nuclei lysis, and reverse transcription of mRNA while incorporating unique barcodes, adapter ligation, and sequencing ( Figure 1 ) [ 51 ].…”

“…In addition, transcriptomically distinct cell populations of the rumen, a tissue that is critical for digestion and feed efficiency and is unique to ruminants, were identified using scRNA-seq in sheep [ 27 , 28 ] and goats [ 28 ] as well as cultured primary epithelial cells in cattle [ 21 ]. In cattle, six cell populations were identified from cultured primary ruminal epithelial cells [ 21 ].…”

“…These results provide critical information about cellular dynamics during the establishment of rumen papillae, which are critical for digestion in sheep and other ruminants [ 27 ]. A comparative study of rumen maturation in sheep and goats identified cell populations at different developmental time points [ 28 ]. This study characterized cellular communication and transcription factor networks critical for rumen development, and correlated changes in cell populations across development to changes in the rumen microbiome [ 28 ].…”

“…While these techniques have been more extensively applied across studies in model organisms and humans, their adoption in livestock species is just beginning. Several studies in cattle, sheep, and goats have utilized sc/snRNA-seq and sc/snATAC-seq to characterize cellular heterogeneity within tissues, track cell population and gene expression changes across developmental time, and profile immune cell populations essential for disease resistance and resilience ( Table 1 , Table 2 and Table 3 ) [ 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 ]. There is immense potential to further utilize these technologies to advance the understanding of cellular and molecular mechanisms governing traits essential for more productive and sustainable livestock while supporting the welfare of these species.…”

“…Understanding the genetic and biological factors that contribute to these traits at single-cell resolution can provide valuable insights into the genetic and epigenetic factors that drive phenotypic variability [ 42 , 43 ]. Furthermore, the application of single-cell genomics in livestock research has the potential to accelerate the pace of genetic improvement by facilitating the identification of cell-type-specific gene expression, along with gene regulatory elements and networks associated with various traits important to livestock production [ 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 ].…”